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https://www.readbyqxmd.com/read/28812732/genome-of-the-pitcher-plant-cephalotus-reveals-genetic-changes-associated-with-carnivory
#1
Kenji Fukushima, Xiaodong Fang, David Alvarez-Ponce, Huimin Cai, Lorenzo Carretero-Paulet, Cui Chen, Tien-Hao Chang, Kimberly M Farr, Tomomichi Fujita, Yuji Hiwatashi, Yoshikazu Hoshi, Takamasa Imai, Masahiro Kasahara, Pablo Librado, Likai Mao, Hitoshi Mori, Tomoaki Nishiyama, Masafumi Nozawa, Gergő Pálfalvi, Stephen T Pollard, Julio Rozas, Alejandro Sánchez-Gracia, David Sankoff, Tomoko F Shibata, Shuji Shigenobu, Naomi Sumikawa, Taketoshi Uzawa, Meiying Xie, Chunfang Zheng, David D Pollock, Victor A Albert, Shuaicheng Li, Mitsuyasu Hasebe
Carnivorous plants exploit animals as a nutritional source and have inspired long-standing questions about the origin and evolution of carnivory-related traits. To investigate the molecular bases of carnivory, we sequenced the genome of the heterophyllous pitcher plant Cephalotus follicularis, in which we succeeded in regulating the developmental switch between carnivorous and non-carnivorous leaves. Transcriptome comparison of the two leaf types and gene repertoire analysis identified genetic changes associated with prey attraction, capture, digestion and nutrient absorption...
February 6, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812710/developmental-constraints-shape-the-evolution-of-the-nematode-mid-developmental-transition
#2
Harel Zalts, Itai Yanai
Evolutionary theory assumes that genetic variation is uniform and gradual in nature, yet morphological and gene expression studies have revealed that different life-stages exhibit distinct levels of cross-species conservation. In particular, a stage in mid-embryogenesis is highly conserved across species of the same phylum, suggesting that this stage is subject to developmental constraints, either by increased purifying selection or by a strong mutational bias. An alternative explanation, however, holds that the same 'hourglass' pattern of variation may result from increased positive selection at the earlier and later stages of development...
March 27, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812685/scallop-genome-provides-insights-into-evolution-of-bilaterian-karyotype-and-development
#3
Shi Wang, Jinbo Zhang, Wenqian Jiao, Ji Li, Xiaogang Xun, Yan Sun, Ximing Guo, Pin Huan, Bo Dong, Lingling Zhang, Xiaoli Hu, Xiaoqing Sun, Jing Wang, Chengtian Zhao, Yangfan Wang, Dawei Wang, Xiaoting Huang, Ruijia Wang, Jia Lv, Yuli Li, Zhifeng Zhang, Baozhong Liu, Wei Lu, Yuanyuan Hui, Jun Liang, Zunchun Zhou, Rui Hou, Xue Li, Yunchao Liu, Hengde Li, Xianhui Ning, Yu Lin, Liang Zhao, Qiang Xing, Jinzhuang Dou, Yangping Li, Junxia Mao, Haobing Guo, Huaiqian Dou, Tianqi Li, Chuang Mu, Wenkai Jiang, Qiang Fu, Xiaoteng Fu, Yan Miao, Jian Liu, Qian Yu, Ruojiao Li, Huan Liao, Xuan Li, Yifan Kong, Zhi Jiang, Daniel Chourrout, Ruiqiang Li, Zhenmin Bao
Reconstructing the genomes of bilaterian ancestors is central to our understanding of animal evolution, where knowledge from ancient and/or slow-evolving bilaterian lineages is critical. Here we report a high-quality, chromosome-anchored reference genome for the scallop Patinopecten yessoensis, a bivalve mollusc that has a slow-evolving genome with many ancestral features. Chromosome-based macrosynteny analysis reveals a striking correspondence between the 19 scallop chromosomes and the 17 presumed ancestral bilaterian linkage groups at a level of conservation previously unseen, suggesting that the scallop may have a karyotype close to that of the bilaterian ancestor...
April 3, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28811309/cellular-and-molecular-mechanisms-coordinating-pancreas-development
#4
REVIEW
Aimée Bastidas-Ponce, Katharina Scheibner, Heiko Lickert, Mostafa Bakhti
The pancreas is an endoderm-derived glandular organ that participates in the regulation of systemic glucose metabolism and food digestion through the function of its endocrine and exocrine compartments, respectively. While intensive research has explored the signaling pathways and transcriptional programs that govern pancreas development, much remains to be discovered regarding the cellular processes that orchestrate pancreas morphogenesis. Here, we discuss the developmental mechanisms and principles that are known to underlie pancreas development, from induction and lineage formation to morphogenesis and organogenesis...
August 15, 2017: Development
https://www.readbyqxmd.com/read/28811188/familial-1p36-3-microduplication-resulting-from-a-1p-9q-non-reciprocal-translocation
#5
Valentine Marquet, Sylvie Bourthoumieu, Amelia Dobrescu, Cécile Laroche-Raynaud, Catherine Yardin
Unlike the 1p36 microdeletion syndrome, which has been extensively described, 1p36 microduplications have rarely been reported. We describe a three years old boy presenting with a severe global developmental delay and a few dysmorphic features. Cytogenetic analyses revealed a maternally inherited 3.35 Mb microduplication of chromosomal band 1p36.3. The maternal grand-father is also carrier of the same chromosomal rearrangement. Interestingly, the duplicated 1p36.3 segment was found to be localized at the telomeric end of the long arms of a chromosome 9, probably deriving from a 1p36...
August 12, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28809827/a-method-for-characterizing-embryogenesis-in-arabidopsis
#6
Jinlin Feng, Ligeng Ma
Given the highly predictable nature of their development, Arabidopsis embryos have been used as a model for studies of morphogenesis in plants. However, early stage plant embryos are small and contain few cells, making them difficult to observe and analyze. A method is described here for characterizing pattern formation in plant embryos under a microscope using the model organism Arabidopsis. Following the clearance of fresh ovules using Hoyer's solution, the cell number in and morphology of embryos could be observed, and their developmental stage could be determined by differential interference contrast microscopy using a 100X oil immersion lens...
August 4, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28809790/genome-wide-organization-and-expression-profiling-of-the-sbp-box-gene-family-in-chinese-jujube-ziziphus-jujuba-mill
#7
Shuang Song, Heying Zhou, Songbai Sheng, Ming Cao, Yingyue Li, Xiaoming Pang
Transcription factors play vital roles in the developmental processes of plants. The SQUAMOSA promoter binding protein (SBP) genes encode a family of plant-specific transcription factors and plays many crucial roles in plant development. In this study, 16 SBP-box gene family members were identified in Ziziphus jujuba Mill. Dongzao (Dongzao), which were distributed over 8 chromosomes. They were classified into seven groups according to their phylogenetic relationships with other SBP-box gene families. Within each group, genes shared similar exon-intron structures and motif locations...
August 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28809400/prenatal-one-carbon-metabolism-dysregulation-programs-schizophrenia-like-deficits
#8
A Alachkar, L Wang, R Yoshimura, A R Hamzeh, Z Wang, N Sanathara, S M Lee, X Xu, G W Abbott, O Civelli
The methionine-folate cycle-dependent one-carbon metabolism is implicated in the pathophysiology of schizophrenia. Since schizophrenia is a developmental disorder, we examined the effects that perturbation of the one-carbon metabolism during gestation has on mice progeny. Pregnant mice were administered methionine equivalent to double their daily intake during the last week of gestation. Their progeny (MET mice) exhibited schizophrenia-like social deficits, cognitive impairments and elevated stereotypy, decreased neurogenesis and synaptic plasticity, and abnormally reduced local excitatory synaptic connections in CA1 neurons...
August 15, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28809033/somitogenesis-and-axial-development-in-reptiles
#9
Cindy Xu, Mariana B Grizante, Kenro Kusumi
Among amniote vertebrates, reptiles display the greatest variation in axial skeleton morphology. Only recently have they been used in gene expression studies of somitogenesis , challenging previous assumptions about the segmentation clock and axial patterning. An increasing number of reptile genomes and transcriptomes are becoming available as next-generation sequencing becomes more affordable. Information regarding gene sequence and structure can be used to design and synthesize labeled riboprobes by in vitro transcription for gene expression analysis by in situ hybridization, thus, enabling the characterization of spatial and temporal expression patterns of genes involved in somitogenesis, a topic of great interest within evolutionary developmental studies of vertebrates...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28809022/enhancer-analyses-using-chicken-embryo-electroporation
#10
Masanori Uchikawa, Naoko Nishimura, Makiko Iwafuchi-Doi, Hisato Kondoh
Chicken embryo electroporation is a powerful tool used to identify and analyze enhancers involved in developmental gene regulation. In this chapter, the basic procedures and underlying principles of enhancer analysis using chicken embryo electroporation are described in the following steps: (1) identification of enhancers in a wide genomic region, (2) determination of the full enhancer region, (3) definition of the core enhancer regions, and (4) analysis of a functional transcription factor binding sequences in the core region...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28809014/genomic-and-transcriptomic-analyses-of-avian-sex-chromosomes-and-sex-linked-genes
#11
Jilin Zhang, Jing Li, Qi Zhou
Sex chromosomes and sex-linked genes usually show unusual features comparing to the rest of the genome and thus are of particular interests to evolutionary and developmental biologists. Here we describe recently developed bioinformatic methods for identifying sex-linked sequences, in a genome without priori linkage information. Some are developed during our course of studying avian genomes. These methods require sequence data, either assembled draft genome or raw sequences derived from the heterogametic sex (e...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808798/genetic-engineering-approach-using-early-vinca-alkaloid-biosynthesis-genes-led-to-increased-tryptamine-and-terpenoid-indole-alkaloids-biosynthesis-in-differentiating-cultures-of-catharanthus-roseus
#12
Abhishek Sharma, Priyanka Verma, Archana Mathur, Ajay Kumar Mathur
Catharanthus roseus today occupies the central position in ongoing metabolic engineering efforts in medicinal plants. The entire multi-step biogenetic pathway of its very expensive anticancerous alkaloids vinblastine and vincristine is fairly very well dissected at biochemical and gene levels except the pathway steps leading to biosynthesis of monomeric alkaloid catharanthine and tabersonine. In order to enhance the plant-based productivity of these pharma molecules for the drug industry, cell and tissue cultures of C...
August 14, 2017: Protoplasma
https://www.readbyqxmd.com/read/28808767/identification-and-expression-analysis-of-micrornas-during-ovule-development-in-rice-oryza-sativa-by-deep-sequencing
#13
Ya Wu, Liyu Yang, Meiling Yu, Jianbo Wang
MicroRNA (miRNA) expression profiles during rice ovule development revealed the possible miRNA-mediated regulation between ovule sporophytic tissue and female gametophyte and the involvement of miRNAs in programmed cell death. MiRNAs are 20-24-nucleotide small RNAs that play key roles in the regulation of many growth and developmental processes in plants. Rice ovule development comprises a series of biological events, which are regulated by complex molecular mechanisms. To gain insight into miRNA-mediated regulation of rice ovule development, Illumina sequencing was used to examine the expression of miRNAs from the megaspore mother cell meiosis stage to the fertilized ovule stage...
August 14, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28808481/cul4b-is-a-novel-prognostic-marker-in-cholangiocarcinoma
#14
Pengyu Li, Lili Zhang, Muyi Yang, Mei Qi, Xing Jin, Bo Han
Cullin 4B (Cul4B), a scaffold protein that assembles the ubiquitin ligase complex, is involved in a wide variety of physiological and developmental processes, such as cell cycle progression, DNA damage response and gene expression regulation. Cul4B is overexpressed in various solid tumors. However, the prognostic value and role of Cul4B in cholangiocarcinoma (CCA) is largely unknown. The present study demonstrated that Cul4B was overexpressed in 21 (26.6%) of 79 patients with intrahepatic CCA, and in 40 (28...
August 2017: Oncology Letters
https://www.readbyqxmd.com/read/28808337/microrna-214-modulates-neural-progenitor-cell-differentiation-by-targeting-quaking-during-cerebral-cortex-development
#15
Pengcheng Shu, Hongye Fu, Xiangyu Zhao, Chao Wu, Xiangbin Ruan, Yi Zeng, Wei Liu, Ming Wang, Lin Hou, Pan Chen, Bin Yin, Jiangang Yuan, Boqin Qiang, Xiaozhong Peng
The accurate generation of an appropriate number of different neuronal and glial subtypes is fundamental to normal brain functions and requires tightly orchestrated spatial and temporal developmental programmes to maintain the balance between the proliferation and the differentiation of neural progenitor cells. However, the molecular mechanism governing this process has not been fully elucidated. Here, we found that miR-214-3p was highly expressed in neural progenitor cells and dynamically regulated during neocortical development...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28808135/mutations-in-eif5b-confer-thermosensitive-and-pleiotropic-phenotypes-via-translation-defects-in-arabidopsis-thaliana
#16
Liyuan Zhang, Xinye Liu, Kishor Gaikwad, Xiaoxia Kou, Fei Wang, Xuejun Tian, Mingming Xin, Zhongfu Ni, Qixin Sun, Huiru Peng, Elizabeth Vierling
The conserved eukaryotic translation initiation factor 5B, eIF5B, is a GTPase that acts late in translation initiation. We found that an Arabidopsis thaliana mutant sensitive to hot temperatures 3 (hot3-1), which behaves as wild type in the absence of stress but is unable to acclimate to high temperature, carries a missense mutation in eIF5B1 gene (At1g76810),, producing a temperature sensitive protein. A more severe, T-DNA insertion allele (hot3-2) causes pleiotropic developmental phenotypes. Surprisingly, Arabidopsis has three other eIF5B genes that do not substitute for eIF5B1; two of these appear to be in the process of pseudogenization...
August 14, 2017: Plant Cell
https://www.readbyqxmd.com/read/28807899/pitx1-directly-modulates-the-core-limb-development-program-to-implement-hindlimb-identity
#17
Stephen Nemec, Maëva Luxey, Deepak Jain, Aurélie Huang Sung, Tomi Pastinen, Jacques Drouin
Forelimbs (FL) and hindlimbs (HL) develop complex musculoskeletal structures that rely on the deployment of a conserved developmental program. Pitx1, a transcription factor gene with expression restricted to HL and absent from FL, plays an important role in generating HL features. The genomic mechanisms by which Pitx1 effects HL identity remain poorly understood, however. Here, we use expression profiling and analysis of direct Pitx1 targets to characterize the HL- and FL-restricted genetic programs and situate the Pitx1-dependent gene network within the context of limb-specific gene regulation...
August 14, 2017: Development
https://www.readbyqxmd.com/read/28807811/clinical-validation-of-a-genome-wide-dna-methylation-assay-for-molecular-diagnosis-of-imprinting-disorders
#18
Erfan Aref-Eshghi, Laila C Schenkel, Hanxin Lin, Cindy Skinner, Peter Ainsworth, Guillaume Paré, Victoria Siu, David Rodenhiser, Charles Schwartz, Bekim Sadikovic
Genomic imprinting involves a DNA methylation-dependent and parent-of-origin-specific regulation of gene expression. Clinical assays for imprinting disorders are genomic locus-, disorder-, and molecular defect-specific. We aimed to clinically validate a genome-wide approach for simultaneous testing of common imprinting disorders in a single assay. Using genome-wide DNA methylation arrays, epigenetic profiles from peripheral blood of patients with Angelman, Prader-Willi, Beckwith-Wiedemann, and Silver-Russell syndrome were compared to a reference cohort of 361 unaffected individuals...
August 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28806941/androgen-receptor-is-expressed-in-mouse-cardiomyocytes-at-prenatal-and-early-postnatal-developmental-stages
#19
Enrique Pedernera, María José Gómora, Iván Meneses, Marlon De Ita, Carmen Méndez
BACKGROUND: Previous studies show that androgens are involved in hypertrophy and excitability of cardiomyocytes and that their effects are mediated through their receptor. The aim of this study was to evaluate the presence of androgen receptor (AR) in mouse heart during prenatal and early postnatal stages. RESULTS: The expression of AR and related genes, alpha myosin heavy chain -Myh6-, beta myosin heavy chain -Myh7- and atrial natriuretic factor -Nppa- was simultaneously evaluated by semiquantitative RT-PCR...
August 14, 2017: BMC Physiology
https://www.readbyqxmd.com/read/28806748/temperature-effects-on-gene-expression-and-morphological-development-of-european-eel-anguilla-anguilla-larvae
#20
Sebastian N Politis, David Mazurais, Arianna Servili, Jose-Luis Zambonino-Infante, Joanna J Miest, Sune R Sørensen, Jonna Tomkiewicz, Ian A E Butts
Temperature is important for optimization of rearing conditions in aquaculture, especially during the critical early life history stages of fish. Here, we experimentally investigated the impact of temperature (16, 18, 20, 22 and 24°C) on thermally induced phenotypic variability, from larval hatch to first-feeding, and the linked expression of targeted genes [heat shock proteins (hsp), growth hormone (gh) and insulin-like growth factors (igf)] associated to larval performance of European eel, Anguilla anguilla...
2017: PloS One
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